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J. Biol. Chem., Vol. 275, Issue 27, 20545-20550, July 7, 2000
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From the Departments of Genetics and Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06510
Received for publication, February 25, 2000, and in revised form, April 25, 2000
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ABSTRACT |
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In the P2-type ATPases, there
is growing evidence that four P-type ATPases, which are found throughout prokaryotic and
eukaryotic cells, use the energy from ATP hydrolysis to pump inorganic cations across cell membranes. In the most abundant subfamily, designated P2, the 100-kDa ATPase polypeptide is embedded
in the lipid bilayer by four hydrophobic segments at the N-terminal end of the molecule and six at the C-terminal end (1). The central hydrophilic region protrudes into the cytoplasm and contains catalytic sites for ATP binding and formation of the characteristic It was proposed more than a decade ago that conformational changes in
the catalytic portion of the P-type ATPases are transmitted into the
membrane via a stalk-like region made up of the cytoplasmic extensions
from some, but not necessarily all, of the transmembrane segments (2).
Recently, the stalk has been directly visualized in cryoelectron
microscopic studies of the sarcoplasmic reticulum Ca2+-ATPase (3) and the plasma membrane
H+-ATPase of Neurospora crassa (4), both at 8-Å
resolution. In the case of the Ca2+-ATPase, the stalk
appeared as a narrow structure connecting the compact, wedge-shaped
cytoplasmic domain with the membrane-spanning segments; it contained
four rod-like densities (very likely Recently, Soteropoulos and Perlin (10) carried out an informative
mutagenesis study of stalk segments 2 and 3 in the yeast plasma
membrane H+-ATPase, a close relative of the
Neurospora enzyme. Their approach was to replace selected
amino acids in S2 (Ile-183 and Gly-186) and S3 (Gly-270 and Thr-287)
with helix-breaking residues, Gly and Pro, in order to test the helical
nature of S2 and S3. At both positions in S2, the mutations proved to
be lethal; at the positions in S3, the cells were viable, but the Pro
replacements led to a significant reduction in ATPase activity. The
authors concluded that the In the present study, we have performed alanine-scanning mutagenesis
along the entire length of S4, again in the yeast
H+-ATPase. S4 almost certainly contributes to the stalk
structure seen by cryoelectron microscopy, and it links the Asp residue that is phosphorylated by ATP to membrane segment 4 (M4). M4 in turn
plays a central role in cation binding and translocation, based on
mutagenesis studies of the sarcoplasmic reticulum
Ca2+-ATPase (11-16), plasma membrane
Ca2+-ATPase (17), Na+,K+-ATPase
(16, 18-20), and gastric H+,K+-ATPase (21).
Consistent with this picture, the mutagenesis results to be described
below provide evidence that stalk segment 4 helps to mediate the
E1/E2 conformational change in the yeast H+-ATPase.
Yeast Strain--
Strain SY4 of Saccharomyces
cerevisiae (MATa, ura3-52, leu2-3,
112, his4-619, sec6-4ts GAL2,
pma1::YIpGAL-PMA1) was used throughout in this study. In strain SY4, the chromosomal copy of the PMA1 gene encoding
the yeast plasma membrane H+-ATPase has been placed under
control of the GAL1 promoter as described previously (22).
SY4 also carries the temperature-sensitive sec6-4 mutation
which, upon incubation at 37 °C, blocks the fusion of secretory
vesicles with the plasma membrane (23).
Mutagenesis--
To introduce mutations into the S4 region of
the H+-ATPase by polymerase chain reaction (24), two
restriction fragments of the PMA1 gene were employed, both
subcloned into a modified Bluescript plasmid (Stratagene, La Jolla,
CA). Mutations from Lys-355 to Ala-370 were introduced into a 615-base
pair BstEII/EcoRI restriction fragment, whereas
mutations from Gly-371 to Leu-375 were introduced into a 495-base pair
StyI/BamHI fragment. After DNA sequencing to
verify the mutation, the restriction fragment was moved into plasmid
PMA1.2 (22). The 3.8-kilobase pair HindIII/SacI
fragment containing the entire pma1-coding region was then
cloned into the yeast expression vector YCp2HSE (22), placing the
mutant allele under control of two tandemly arranged heat-shock
elements. Finally, the plasmids were transformed into yeast strain SY4
(see above) according to the method of Ito et al. (25).
Isolation of Secretory Vesicles and Quantitation of Expressed
ATPase--
Transformed SY4 cells were grown to mid-exponential phase
(A600 ~1) at 23 °C in supplemented minimal
medium containing 2% galactose, shifted to medium containing 2%
glucose for 3 h, and then heat-shocked at 39 °C for an
additional 2 h. The cells were harvested and washed, and secretory
vesicles were isolated and suspended in 0.8 M sorbitol, 1 mM EDTA, 10 mM triethanolamine/acetic acid, pH
7.2, as described previously (26). To determine the level of expressed
PMA1 protein, secretory vesicles (5-20 µg) were subjected to
SDS-polyacrylamide gel electrophoresis and immunoblotted. Quantitative
PhosphorImager (Bio-Rad) analysis was carried out at two protein
concentrations within the linear range, and the expression level was
calculated from the average of two or more determinations.
ATP Hydrolysis--
Unless otherwise noted, ATP hydrolysis was
assayed at 30 °C in 0.5 ml of 50 mM
MES1/Tris, pH 5.7, 5 mM KN3, 5 mM Na2ATP, 10 mM MgCl2, and an ATP-regenerating system (5 mM phosphoenolpyruvate and 50 µg/ml pyruvate kinase). The
reaction was terminated after 20-40 min, and the release of inorganic
phosphate from ATP was determined by the method of Fiske and Subbarow
(27). Specific activity was calculated as the difference between ATP
hydrolysis in the absence and in the presence of 100 µM
sodium orthovanadate, a potent inhibitor of P-type ATPases. IC50 values for vanadate inhibition were determined by
measuring ATP hydrolysis in the presence of increasing concentrations
of vanadate. For determination of Km values,
Na2ATP was varied between 0.15 and 7.5 mM with
MgCl2 always in excess of ATP by 5 mM; actual
concentrations of MgATP were calculated by the method of Fabiato and
Fabiato (28). To determine the pH optimum for ATP hydrolysis, the pH of
the assay media was adjusted to values between 5.2 and 7.5 with Tris base.
ATP hydrolysis was also assayed under conditions similar to that used
for quantitation of proton transport (see below), as described
previously (29). Briefly, secretory vesicles (5-10 µg of protein)
were diluted into 200 µl of 0.6 M sorbitol, 0.1 M KCl, 20 mM HEPES/KOH, pH 6.7, Na2ATP (0.3 to 3.0 mM), and MgCl2 (5 mM excess over the ATP concentration) at 30 °C. The
reaction was stopped after 20-40 min by addition of trichloroacetic
acid to a final concentration of 5%, and inorganic phosphate was determined.
Proton Transport and Fluorescence
Quenching--
ATP-dependent proton transport was assayed
by measuring the initial rate of acridine orange fluorescence quenching
as described previously (29). The specific initial rate of quenching
was adjusted for the level of ATPase expression and reported as a percentage of the wild-type rate. In order to examine the coupling of
proton transport to ATP hydrolysis, the initial rate of fluorescence quenching was determined over a range of ATP concentrations and plotted
as a function of the rate of ATP hydrolysis, assayed under similar
conditions (see above).
Trypsinolysis--
Limited trypsinolysis was performed on
isolated secretory vesicles as described previously (30). Vesicles were
suspended at 0.5 mg/ml in 20 mM Tris-HCl, pH 7.0, and 5 mM MgCl2. Following preincubation at 30 °C
for 5 min in the presence of 0, 1, 10, or 100 µM
orthovanadate, tosylphenylalanyl chloromethyl ketone-treated trypsin
was added (trypsin/protein ratio of 1:4), and the incubation was
continued for 20 min. The reaction was terminated by the addition of 1 mM diisopropyl fluorophosphate, and the products were
analyzed by immunoblotting with polyclonal antiserum against the ATPase.
Protein Determination--
Protein concentrations were
determined by the method of Lowry et al. (31) as modified by
Ambesi et al. (26), with bovine serum albumin as standard.
Selection of Residues for Mutagenesis--
The goal of the present
study was to explore the functional role of amino acid residues
throughout stalk segment 4 (S4), which links membrane segment 4 (M4)
with the phosphorylation site (Asp-378) of the yeast plasma membrane
H+-ATPase (Fig. 1). Residues
from Lys-355 to Leu-375 were subjected to alanine-scanning mutagenesis,
filling in the 21-amino acid stretch between previously published
studies of M4 (Tyr-325 through Ala-354; Ref. 29) and the
phosphorylation domain (Cys-376 through Thr-384; Refs. 32 and 33). With
the exception of Ala-358, Ala-365, and Ala-370, which were replaced
with Ser, each residue was changed to Ala. Each mutant allele was
cloned into the expression vector YCp-2HSE, transformed into yeast
strain SY4, and expressed under the control of a heat-shock promoter
after turning off the wild-type PMA1 allele (22). Secretory
vesicles containing newly synthesized mutant ATPase were then isolated
and characterized (26).
Expression and ATP Hydrolysis--
As summarized in Table
I (top part), quantitative
immunoblotting revealed that Ala/Ser substitutions in S4 had only a
modest effect on biogenesis, with mutant H+-ATPases
reaching the secretory vesicles at 35-101% of the amount seen in the
wild-type control. Likewise, 19 of 21 mutant enzymes clearly retained
the ability to hydrolyze ATP, with specific activities ranging from 27 to 118% after correction for the level of expression in the vesicles.
Only two of the mutants showed more serious defects in ATP hydrolysis
as follows: L369A (12%) and I374A (16%), and even in these cases, the
uncorrected activities were 4-5-fold greater than the background
values measured in the empty plasmid control. Thus, none of the
residues in S4 appeared to be completely essential for ATP hydrolysis,
although most of the mutations caused at least a 50% decrease in the
rate of hydrolysis.
Proton Transport--
Given that S4 physically links the
phosphorylated Asp residue to the membrane, it was important to examine
the effects of the Ala/Ser substitutions on the ability of the ATPase
to transport protons. This was measured by fluorescence quenching of
the pH-sensitive dye, acridine orange (Table I, top part).
In four of the mutants (K356A, L369A, I374A, and L375A),
ATP-dependent quenching was clearly above background, but
the activities were so low that quantitative determinations were not
possible. In one mutant (E367A), the initial rate of proton transport
(83% of wild type) appeared to exceed the rate of ATP hydrolysis (46%
of wild type). Closer examination of this mutant seemed warranted,
given the fact that Glu-367 is strongly conserved among
P2-ATPases (see Fig. 1). When proton transport was measured
over a range of ATP concentrations, however, and the initial rates were
plotted as a function of ATP hydrolysis assayed under the same
conditions, the data for E367A (like the data for three other mutants)
proved to be very similar to the wild-type control (Fig.
2). It later became obvious that the
discrepancy in Table I could be accounted for by the abnormal pH
optimum of the E367A ATPase (see legend to Fig. 2 and below). For all
of the remaining mutants, the initial rate of ATP-dependent quenching closely paralleled that of ATP hydrolysis (Table I), suggesting that the substitutions had little or no effect on the coupling between transport and hydrolysis.
Vanadate Resistance--
Each of the mutant ATPases was next
examined for changes in sensitivity to inorganic orthovanadate, an
inhibitor that binds tightly to the E2 conformation of
P-type ATPases. Here, a striking result was obtained; of the 21 mutants
studied, 9 showed a very significant degree of vanadate resistance,
with IC50 values above 10 µM (Table
II, top part). The resistant
mutations began at position 360 and continued (with interruptions)
through position 374. Upon closer inspection of this region, it was
apparent that 4 of the 6 mutants still sensitive to vanadate carried
substitutions of Ser for Ala or Ala for Ser. Because a less
conservative substitution at one of these positions (S368F) had
previously been shown to produce a highly vanadate-resistant enzyme
(34), it seemed worthwhile to make further replacements of Ser-364,
Ala-365, and Ala-370. To define the ends of the region, Ile-359,
Val-372, and Glu-373 were also included.
Among the additional mutants that were tested, all but one (V372F) were
expressed in secretory vesicles at 43% or more of the wild-type level,
and all but two (A370L and V372F) had measurable rates of ATP
hydrolysis (Table I, bottom part). Furthermore, for every
mutant with sufficient activity to be assayed, there was a close
correspondence between the initial rate of ATP hydrolysis and the
initial rate of ATP-dependent proton transport (Table I),
indicating that these substitutions (like the initial set described
above) had little or no effect on the coupling between hydrolysis and transport.
In five of the additional mutants (I359F, S364D, A365F, A365L, and
A370F), the IC50 value for vanadate rose above 10 µM (Table II, bottom part), confirming that
substantial vanadate resistance could be observed at these positions as
well. The distribution of resistance along S4 is illustrated in Fig.
3A, which demonstrates that
the 13-amino acid stretch from Ile-359 through Gly-371 can undergo
mutations that elevate the IC50 more than 5-fold above the
wild-type value.
Other Kinetic Properties--
In previous mutagenesis studies of
the yeast H+-ATPase, vanadate resistance has frequently
been accompanied by a reduction in the apparent Km
value for MgATP and a rise in pH optimum (29, 30). This
"coordinated" phenotype has been interpreted as a shift in
equilibrium from the vanadate-sensitive E2 conformation toward the E1 conformation, where MgATP and the transported
proton are expected to bind with higher affinity than in
E2. In the present study, 6 of the 14 vanadate-resistant
mutants in the stalk 4 region (I359F, S364D, I366A, E367A, L369A, and
A370F) displayed Km values of 0.5 mM or
lower, representing at least a 3-fold change from the value seen in the
wild-type control; six additional mutants (Q361A, K362A, L363A, A365F,
A365L, and I374A) gave smaller but reproducible reductions to 0.6-0.9
mM (Table II). Thus, a strong but not complete correlation
could be seen between vanadate resistance and a decreased
Km for MgATP (Fig. 3B).
Not surprisingly, given the many ways in which the pH dependence of the
H+-ATPase might be altered, the situation was less
clear-cut with regard to pH optimum. Four of the vanadate-resistant
mutants (L363A, I366A, E367A, and A370F) displayed a conspicuous
alkaline shift of 0.3 to 0.6 pH units (Table II). The rest retained an
essentially normal pH optimum, except for a few with a minor shift in
the acid direction (e.g. K362A).
E1 to E2 Conformational Change Assessed by
Limited Trypsinolysis--
If the cluster of kinetic changes seen in
many of the stalk 4 mutants reflects a shift in equilibrium from the
vanadate-sensitive E2 conformation toward the vanadate-insensitive E1
conformation, it should be possible to detect the shift by limited
trypsinolysis (29, 30). In the experiment of Fig.
4, secretory vesicles were incubated with
trypsin for 20 min in the presence of 0, 1, 10, or 100 µM
vanadate. The reaction was stopped by the addition of diisopropyl
fluorophosphate (1 mM), and the digestion products were
separated by SDS-polyacrylamide gel electrophoresis and immunoblotted with anti-PMA1 antibody. Under the conditions of the experiment, the wild-type ATPase displayed significant protection by vanadate, with
the accumulation of 97-, 70-, and 60-kDa fragments. By contrast, the
fragments were barely visible in E367A and not seen at all in I366A,
consistent with the idea that the mutant enzymes had difficulty
reaching the vanadate-protectable E2 conformation.
This study reports an impressive stretch of 13 consecutive
vanadate-resistant mutations in stalk segment 4 of the yeast PMA1 H+-ATPase. While similar mutations have been described
previously for the yeast ATPase (29, 30, 32, 35-37), they have been scattered throughout the 100-kDa polypeptide, with no discernible structural or functional pattern (Fig.
5). The cluster in S4 therefore deserves
special interest.
-helical stalk segments connect the
cytoplasmic part of the molecule, responsible for ATP binding and
hydrolysis, to the membrane-embedded part that mediates cation
transport. The present study has focused on stalk segment 4, which
displays a significant degree of sequence conservation among
P2-ATPases. When site-directed mutants in this region of
the yeast plasma membrane H+-ATPase were constructed and
expressed in secretory vesicles, more than half of the amino acid
substitutions led to a severalfold decrease in the rate of ATP
hydrolysis, although they had little or no effect on the coupling
between hydrolysis and transport. Strikingly, mutant ATPases bearing
single substitutions of 13 consecutive residues from Ile-359 through
Gly-371 were highly resistant to inorganic orthovanadate, with
IC50 values at least 10-fold above those seen in the
wild-type enzyme. Most of the same mutants also displayed a significant
reduction in the Km for MgATP and an increase in
the pH optimum for ATP hydrolysis. Taken together, these changes in
kinetic behavior point to a shift in equilibrium from the
E2 conformation of the ATPase toward the E1
conformation. The residues from Ile-359 through Gly-371 would occupy
three full turns of an
-helix, suggesting that this portion of stalk
segment 4 may provide a conformationally active link between catalytic
sites in the cytoplasm and cation-binding sites in the membrane.
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INTRODUCTION
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
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DISCUSSION
REFERENCES
-aspartyl phosphate intermediate.
-helices), which were
tentatively identified as stalk segments 2-5 (3). The
Neurospora H+-ATPase was strikingly similar to
the Ca2+-ATPase in its membrane region, but the cytoplasmic
portion was noticeably less compact, and instead of a single stalk,
there were several apparent connections between the cytoplasmic portion and the membrane (4). As the authors pointed out (3-5), the two
structures may represent different conformational states, since the
Ca2+-ATPase was crystallized in the presence of
decavanadate and the H+-ATPase, in the absence of added
ligands. Indeed, there is compelling evidence that the reaction cycle
of the P-ATPases alternates between two major conformations
(E1 and E2), that are different enough to be
distinguished from one another by a variety of biochemical and
biophysical methods (6) including proteolytic digestion patterns (7-9).
-helical nature of S2, and to a lesser
extent that of S3, may help to stabilize the stalk and/or promote the proper conformational interaction between the cytoplasmic and membrane-embedded portions of the ATPase.
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EXPERIMENTAL PROCEDURES
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
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DISCUSSION
REFERENCES
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RESULTS
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
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REFERENCES

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Fig. 1.
Sequence alignment of stalk segment 4. A, the 30-amino acid stretch from the beginning of stalk
segment 4 to the end of the phosphorylation region has been aligned for
9 representative P2-ATPases. Swiss-Prot sequence accession
numbers are (top to bottom) as follows: P05030,
P07038, P09627, P54210, P20649, Q00804, P13585, P04074, and P09626. For
clarity, residues identical to the yeast PMA1 sequence are replaced
with a period. The catalytic Asp residue is indicated in
bold type. B, the Garnier-Robson
secondary structure prediction for the yeast PMA1 H+-ATPase
was determined using the Peptide Structure program of the University of
Wisconsin Genetics Computer Group. Residues likely to assume an
-helical structure are indicated by H,
-turns by
T, and indeterminate structure by periods.
Effect of mutations in stalk segment 4 on expression, ATP hydrolysis,
and proton transport

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Fig. 2.
Coupling between ATP hydrolysis and proton
transport in S4 mutants. The initial rate of fluorescence
quenching (proton transport) was determined over a range of ATP
concentrations (0.3-3.0 mM) and plotted as a function of
the rate of ATP hydrolysis measured under similar conditions as
described previously (26). The data represent the average of 2-4
independent preparations, and the lines were drawn by least squares
analysis.
Kinetic properties of stalk 4 mutants

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Fig. 3.
Kinetic parameters for mutants of stalk
segment 4. Mutant ATPases were expressed in secretory vesicles and
assayed for ATP hydrolysis in the presence of increasing concentrations
of vanadate (A) or MgATP (B). The
IC50 and Km values were determined by
standard methods ("Experimental Procedures") and displayed as a
function of S4 sequence position. Values for S368F come from a previous
study by Harris et al. (34).

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Fig. 4.
Trypsinolysis of I366A and E367A.
Secretory vesicles were incubated for 20 min at a trypsin/protein ratio
of 1:4 in the presence of 0, 1, 10, or 100 µM vanadate,
and the reaction was terminated by the addition of 1 mM
diisopropyl fluorophosphate as described under "Experimental
Procedures." The fragment pattern was analyzed by SDS-polyacrylamide
gel electrophoresis and immunoblotting. WT, wild type.
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES

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Fig. 5.
Location of vanadate-resistant mutations in
the yeast plasma-membrane H+-ATPase. Mutations that
confer a 5-fold or greater increase in vanadate resistance are
indicated by solid circles. P, phosphorylation
site (Asp-378).
At the structural level, S4 is customarily depicted as an
-helix,
acting with three other stalk helices to connect the cytoplasmic and
membrane-embedded portions of the ATPase. Evidence for the
-helical
nature of S4 came originally from the use of standard algorithms (as
reviewed in Ref. 38) and has since been reinforced by cryoelectron
microscopy of the sarcoplasmic reticulum Ca2+-ATPase, where
an
-helical backbone was found to fit comfortably into each of four
rod-like densities within the stalk region (5). Significantly, however,
the residues represented by the vanadate-resistant mutants from Ile-359
through Gly-371 would not be restricted to one face of such a helix;
instead, they would occupy three full turns near the middle of S4.
Functionally, it seems likely that the mutations cause a shift in
E1-E2 equilibrium toward the
vanadate-insensitive E1 conformation, given the fact that
most of them display coordinated changes in the Km
value for MgATP and the pH optimum of the H+-ATPase. In an
earlier paper (29), we described three similar mutants, spaced at
intervals along transmembrane segment M4 (I332A, V336A, and V341A).
Likewise, Blostein and co-workers (39, 40) have pointed out that a
shift in E1-E2 equilibrium could explain the
kinetic behavior of two Na+,K+-ATPase mutants:
E233K, located in the M2-M3 cytoplasmic loop (39, 40), and
1M32, a
deletion mutant lacking 32 amino acids at the N terminus. In both
mutants, vanadate resistance was accompanied by a decrease in the
Km value for MgATP and by marked K+
activation of Na-ATPase activity at micromolar ATP concentrations, a
condition under which the E2(K) to E1 step is
normally rate-limiting.
The concentration of E1-E2 mutants in stalk segment 4 of the yeast H+-ATPase suggests that S4 may provide a critical, conformationally mobile link between the cytoplasmic phosphorylation site and cation-binding sites in the membrane. Independent evidence for this idea has come from mutagenesis studies by Inesi and co-workers (41) on stalk segment 4 of the sarcoplasmic reticulum Ca2+-ATPase. Here, single substitutions of conserved S4 residues significantly slowed the rate of ATP hydrolysis and Ca2+ uptake, even though measurable levels of phosphorylated intermediate were formed (41). Single substitutions of non-conserved residues were less damaging, but multiple substitutions of such residues interfered with the Ca2·E1P to Ca2·E2 transition (as reflected by the rate of phosphoenzyme turnover) and the E1 to E2 transition (as reflected by the time course of EGTA inactivation, Ref. 42). Thus, once again it seems likely that stalk 4 has a profound influence on rate-limiting conformational transitions.
To visualize the way in which S4 performs this function, high
resolution structures for both the E1 and E2
conformations will be required. Reporter groups engineered into
specific locations along S4 will also help to track the conformational
changes; studies along these lines are presently under way in several
laboratories including our own.
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FOOTNOTES |
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* This work was supported by a Fogarty postdoctoral fellowship (to M. M.) and by NIGMS Research Grant GM15761 from the National Institutes of Health (to C. W. S.).The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
To whom correspondence and reprint requests should be addressed:
Depts. of Genetics and Cellular & Molecular Physiology, Yale University
School of Medicine, 333 Cedar St., New Haven, CT 06510. Tel.:
203-737-1770; Fax: 203-737-1771.
Published, JBC Papers in Press, May 1, 2000, DOI 10.1074/jbc.M00168220
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ABBREVIATIONS |
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The abbreviation used is: MES, 4-morpholineethanesulfonic acid.
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